Quite by chance I have just received an update of a review I did for [a gold open access scientific journal]. I omit all confidential info:
Dear Dr. Murray-Rust,
Thank you for your review of this manuscript. The Editor has made a decision on this paper and a copy of the decision letter can be found below.
You can also access your review comments and the decision letter by logging onto the Editorial Manager as a Reviewer.
[Dear Author… ]
Before your manuscript can be formally accepted, your files will be checked by the [publisher’s] production staff. Once they have completed these checks, they will return your manuscript to you so that you may attend to their requests and make any changes that you feel necessary.
To speed the publication of your paper you should look very closely at the PDF of your manuscript. You should consider this text to have the status of a production proof. Your paper will be tagged and laid out to produce professional PDF and online versions. However, the text you have supplied will be faithfully represented in your published manuscript exactly as you have supplied it.
So as far as the author and reviewer are concerned everything is driven by PDF (confirming Cameron’s experience). PDF is a well-known destroyer of semantic information. This, of course, is common to all publishers. We have allowed them to create this monster and force it on us.
PDF holds back the development of semantically supported science.
As much as I agree that most publishers are still overly focussed on the PDF representation of articles, blaming the PDF is, surely, like blaming pen and ink, or the printing press for holding back scientific communication. The PDF is just a human readable representation of a scientific work, much as HTML is. They both have different pros and cons (though, interestingly in the previous example you gave (/pmr/2011/07/16/how-to-share-data-and-how-not-to/) where PLoSOne had converted tables into bitmaps in the HTML representation, the tables were still at least selectable text in the PDF representation, and as has been pointed out in the comments, quite nicely machine readable in the XML version). Although it’s possible to shove a whole load of semantic information into a PDF, this is rarely done by publishers (and in any case, doesn’t really move things much further forward).
The basic issue is that humans and machines work on very different representations: humans like nicely formatted text and figures to read on screen or paper, and extract the ‘semantics’ automatically; machines like XML or RDF, and need explicitly encoded semantics (which very few humans can comprehend). At the moment there is no viable format that works well for both human and machine, and until we have one that is accepted by writers, readers and publishers, we’ll have to make do with tools that translate between these formats. Maybe Scholarly HTML will become this. That would be nice. In the PLoSOne example, all the information one might want was actually available, but it was dispersed amongst several files, and the interface didn’t make this obvious, or provide tools to allow a human to easily access the (non human readable) tabular data in the XML whilst looking at the (human readable) PDF or HTML.
The problem has to be is in the process, and the lack of integration between representations, not any one specific file format.
You might like this antibody though : http://www.antibodies-online.com/antibody/438520/anti-PDF/
Thanks very much Steve,
All agreed.
I am not blaming the PDF per se, it is shorthand for blaming some human insisting that we use it where it is not appropriate. Researchers still complete their safety forms in ink and I would rather be safe than dogmatic.
The problem is that people see PDF as a single solution to a compex problem. Because it has lower cost that doing things properly it’s obviously attractive to promote as a monoculture
I very much agree — I think the main challenge is finding a new paradigm that suits the needs of publishers, academics and (importantly) funding bodies all at the same time. And whatever happens next, it will need to encompas file/exchange formats AND metrics. If we miss out any of these players or components, it’ll all be for nothing. At the moment the academic community is involved in a strange global game of Prisoner’s Dilemma: if all academics / scientists jump onto a new paradigm at the same time ( stop publishing in closed access / stop reviewing for closed access / only publishe ‘semantically’ / only use ‘new’ formats of dissemination / etc ) then we all win in a big way. But… if only some people take the risk, then the whole venture almost certainly fails because those who didn’t take the risk get the grant money to continue their work and the rest of us vanish into obscurity… and so the dance goes on.
[in a shameless self-promoting plug, there’s a long version of my previous reply in an article at http://dx.doi.org/10.1087/20110309 . Open Access, of course. ]
I’ve always seen PDF as a by-product of the publishers’ workflow, the easiest way to get DTP software to talk to printers. When ‘ejournals’ became popular, I assumed publishers simply lowered the resolution of the output and dumped them onto the web, a cheap if ineffective means of online publishing. Its desktop convenience is also to blame.
For mainstream publishing, the advent of a multitude of e-reader and tablet devices has changed this, publishers now need re-purposable XML to output in the many competing ebook formats, as well as PDF for print. This has required an expensive ‘retooling’ in terms of publishing software and a rethink in skills for publishing houses.
It remains to be seen if this leap will continue into scientific publishing, after all, PDF articles are still consumed every day, but it may happen. It would require a skillset and tools that allows those involved in the publication to check the validity of markup at every stage, probably easier than ‘closely examining’ a PDF.
PDFs cause numerous problems with digital preservation, there are ample reasons to move on beyond this terrible format.
Thanks Ed,
I hadn’t realised PDF was awful for preservation as well, so make this widely known!